Hi I am trying to do peak-calling using MACS for some of my H3K4me3 ChIP-seq data. Using the default p-value of 1e-5 I only obtained 500+ peaks. But if I change the p-value to 1e-4 I got 1500+ peaks and by increasing it more to 1e-3 I got 7000+ peaks! My question is how do I know which is the best p-value to use? I would like to get more peaks but I also don't want any false positive peaks. Thanks for your help!
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There is no best number and it completely depends on your data set. Load the data onto a genome visualizer and look at the peaks it is calling. Use your best judgement and validate by qPCR. Fold enrichment is another important and easy to understand parameter to consider.--------------
Ethan
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dgrayson, if you use the -w option when running MACS you will generate a wig file which can be uploaded and visualized on a genome browser. I like to use the -w option with the -S option so that I only generate a single wig file instead of one for each chromosome.
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